tagzygosity should only tag variants carried by affected individuals

[williamrowell]

Added a parameter, affected, to tagzygosity. Comma-delimited list of affected individuals. Only affected individuals are considered for tagging.

Needs work before merging. This should probably be an optional input. Also, I deleted all of the large compressed resources because the repo was taking forever to clone. We can revert those changes before merging, but should also consider hosting the files on Zenodo instead.

Opinions on the idea of the change? Any other suggestions?

[amwenger]

Added a parameter, affected, to tagzygosity. Comma-delimited list of affected individuals. Only affected individuals are considered for tagging.

I like the idea, and the implementation looks good too. I suggest using a more general parameter name - --samples instead of --affected - since svpack is more general than rare-disease analysis.

Also, I deleted all of the large compressed resources because the repo was taking forever to clone. We can revert those changes before merging, but should also consider hosting the files on Zenodo instead.

Good point. These files are already in https://zenodo.org/records/8415406. Could you update the README.md to reference that Zenodo record and remove the binary files from the repo?